Thanks a lot for all the help in the previous topic.
Now we are having a problem with cluster() simply quitting after running for a while (about two hours or so) without any message or error log. Any ideas why?

Weird - remind me is this in windows/mac/linux? Also, how big is your distance matrix and how much RAM do you have?

Its Unix with 16 Gb RAM. The size of the distance matrix is 21,589,683,246.

So you’re trying to cram a 21 GB file into 16 GB of RAM :). Are you using a distance cutoff when you run the read.dist? I would suggest maybe using 0.20 and going from there. Also, make sure to consult the Costello example analysis to see how we manage data to provide a robust analysis that should be doable on most computers with most datasets.